Hey There,
Unless it's a permissions issue (where you can't delete the folders as the user that runs the batch file) is it possible that you're trying this at the command line as proof-of-concept for the batch file.
If you're doing command line testing, although the variable MUST be %%A in your batch file, it has to be %A when run from the command line (why? I haven no idea
c:\cygwin\tmp\test>dir
Volume in drive C has no label.
Volume Serial Number is F08F-D325
Directory of c:\cygwin\tmp\test
12/16/2008 10:15 PM <DIR> .
12/16/2008 10:15 PM <DIR> ..
12/16/2008 10:15 PM <DIR> test1
0 File(s) 0 bytes
3 Dir(s) 4,743,143,424 bytes free
c:\cygwin\tmp\test>FOR /D %A IN (C:\cygwin\tmp\test\*) DO rmdir /s /q %A
c:\cygwin\tmp\test>rmdir /s /q C:\cygwin\tmp\test\test1
c:\cygwin\tmp\test>dir
Volume in drive C has no label.
Volume Serial Number is F08F-D325
Directory of c:\cygwin\tmp\test
12/16/2008 10:16 PM <DIR> .
12/16/2008 10:16 PM <DIR> ..
0 File(s) 0 bytes
2 Dir(s) 4,743,143,424 bytes free
c:\cygwin\tmp\test>
Best wishes,
Mike